The impact of the spectral dimension of hyperspectral datasets on plant disease detection

Precision Agriculture as an information based approach requires explicit spatial information about the within field heterogeneities for site-specific applications. Thus, the usage of cost-intensive agrochemicals and the impact on the environment can be significantly reduced. Spectroscopic approaches are thereby a promising tool for providing fast and precise information on a local to regional level. In this thesis, the impact of hyperspectral near-range and remote sensing data for crop stress detection will be observed since spectroscopic approaches are of great interest for Precision Agriculture. Two greenhouse experiments and three field experiments were conducted with spectroscopic measurements to examine possibilities and limitations of hyperspectral data. The data were acquired using a near-range non-imaging spectrometer (ASD Fieldspec 3) and a near-range imaging spectrometer (ImSpec V10E) in the greenhouse, or were acquired by the airborne sensor systems HyMapTM, ROSIS or AISA for the field experiments. The methodical foci thereby are the improvement of binary detection approaches, discriminating 'vital' and 'infected' wheat stands or parts of wheat stands, and quantification approaches to estimate disease severities at canopy level. This thesis examines the spectral dimension of hyperspectral data for crop stress detection by assessing data redundancy and defining spectral necessities. Different feature selection methods were tested for their suitability in reducing the high amount of spectral data without losing significant information. Conventional classification approaches and recent developments, such as support vector machines for classification (SVM), were thereby tested based on the identified spectral subsets to assess the status of different wheat stands. By focusing on phenomenon-specific spectral bands, stressed wheat stands could successfully be identified with high accuracies. Using optimal band combinations could even increase classification accuracies. The results showed that not the entire spectrum of hyperspectral data is necessary for the detection of fungal infections in wheat. These findings are particularly interesting for future spectral sensor design and remote sensing missions that are aiming at the provision of spatial information for agricultural practice. The ability of hyperspectral data in quantifying the severity of fungal diseases was observed. Site-specific fungicide treatments based on application maps are technically possible and doses can be adjusted if the maps provide information about the health status of the crops. Crop growth anomalies caused by fungal infections were observed, which differed significantly within one field. The derivation of disease severities based on hyperspectral near-range and remote sensing data were examined using classification approaches and support vector machines for regression (SVR). Fungal infections of wheat stands in the greenhouse and wheat stands in the field could be quantified with a high level of certainty. The results are very promising and the findings may be of great interest for agricultural questionnaires and automatic phenotyping approaches, since the presented approaches are fast and non-destructive. Spatial maps with continual disease severity data could be derived, which can be used to generate application maps for agricultural practice. Since the study shows that a reduction of hyperspectral data to a few but specifically selected spectral bands can improve the classification accuracies or regression analyses, a preliminary feature selection should be considered when working with hyperspectral remote sensing data. Agricultural and geographical approaches that are based on spatial-spectral information may thus profit from a faster and more reliable extraction of information. The study shows great advantages of the usage of hyperspectral imaging data but also the necessity of advanced and innovative analyzing methods

Detection of multi-tomato leaf diseases (late blight, target and bacterial spots) in different stages by using a spectral-based sensor.

Several diseases have threatened tomato production in Florida, resulting in large losses, especially in fresh markets. In this study, a high-resolution portable spectral sensor was used to investigate the feasibility of detecting multi-diseased tomato leaves in different stages, including early or asymptomatic stages. One healthy leaf and three diseased tomato leaves (late blight, target and bacterial spots) were defined into four stages (healthy, asymptomatic, early stage and late stage) and collected from a field. Fifty-seven spectral vegetation indices (SVIs) were calculated in accordance with methods published in previous studies and established in this study. Principal component analysis was conducted to evaluate SVIs. Results revealed six principal components (PCs) whose eigenvalues were greater than 1. SVIs with weight coefficients ranking from 1 to 30 in each selected PC were applied to a K-nearest neighbour for classification. Amongst the examined leaves, the healthy ones had the highest accuracy (100%) and the lowest error rate (0) because of their uniform tissues. Late stage leaves could be distinguished more easily than the two other disease categories caused by similar symptoms on the multi-diseased leaves. Further work may incorporate the proposed technique into an image system that can be operated to monitor multi-diseased tomato plants in fields

Role of Hyperspectral imaging for Precision Agriculture Monitoring

In the modern era precision agriculture has started emerging as a new revolution. Remote sensing is generally regarded as one of the most important techniques for agricultural monitoring at multiple spatiotemporal scales. This has expanded from traditional systems such as imaging systems, agricultural monitoring, atmospheric science, geology and defense to a variety of newly developing laboratory-based measurements. The development of hyperspectral imaging systems has taken precision agriculture a step further. Because of the spectral range limit of multispectral imagery, the detection of minute changes in materials is significantly lacking, this shortcoming can be overcome by hyperspectral sensors and prove useful in many agricultural applications. Recently, various emerging platforms also popularized hyperspectral remote sensing technology, however, it comes with the complexity of data storage and processing. This article provides a detailed overview of hyperspectral remote sensing that can be used for better estimation in agricultural applications

A comprehensive review of 3D convolutional neural network-based classification techniques of diseased and defective crops using non-UAV-based hyperspectral images

Hyperspectral imaging (HSI) is a non-destructive and contactless technology that provides valuable information about the structure and composition of an object. It can capture detailed information about the chemical and physical properties of agricultural crops. Due to its wide spectral range, compared with multispectral- or RGB-based imaging methods, HSI can be a more effective tool for monitoring crop health and productivity. With the advent of this imaging tool in agrotechnology, researchers can more accurately address issues related to the detection of diseased and defective crops in the agriculture industry. This allows to implement the most suitable and accurate farming solutions, such as irrigation and fertilization before crops enter a damaged and difficult-to-recover phase of growth in the field. While HSI provides valuable insights into the object under investigation, the limited number of HSI datasets for crop evaluation presently poses a bottleneck. Dealing with the curse of dimensionality presents another challenge due to the abundance of spectral and spatial information in each hyperspectral cube. State-of-the-art methods based on 1D- and 2D-CNNs struggle to efficiently extract spectral and spatial information. On the other hand, 3D-CNN-based models have shown significant promise in achieving better classification and detection results by leveraging spectral and spatial features simultaneously. Despite the apparent benefits of 3D-CNN-based models, their usage for classification purposes in this area of research has remained limited. This paper seeks to address this gap by reviewing 3D-CNN-based architectures and the typical deep learning pipeline, including preprocessing and visualization of results, for the classification of hyperspectral images of diseased and defective crops. Furthermore, we discuss open research areas and challenges when utilizing 3D-CNNs with HSI data

Retrieval of Leaf Area Index (LAI) and Soil Water Content (WC) Using Hyperspectral Remote Sensing under Controlled Glass House Conditions for Spring Barley and Sugar Beet

Leaf area index (LAI) and water content (WC) in the root zone are two major hydro-meteorological parameters that exhibit a dominant control on water, energy and carbon fluxes, and are therefore important for any regional eco-hydrological or climatological study. To investigate the potential for retrieving these parameter from hyperspectral remote sensing, we have investigated plant spectral reflectance (400-2,500 nm, ASD FieldSpec3) for two major agricultural crops (sugar beet and spring barley) in the mid-latitudes, treated under different water and nitrogen (N) conditions in a greenhouse experiment over the growing period of 2008. Along with the spectral response, we have measured soil water content and LAI for 15 intensive measurement campaigns spread over the growing season and could demonstrate a significant response of plant reflectance characteristics to variations in water content and nutrient conditions. Linear and non-linear dimensionality analysis suggests that the full band reflectance information is well represented by the set of 28 vegetation spectral indices (SI) and most of the variance is explained by three to a maximum of eight variables. Investigation of linear dependencies between LAI and soil WC and pre-selected SI's indicate that: (1) linear regression using single SI is not sufficient to describe plant/soil variables over the range of experimental conditions, however, some improvement can be seen knowing crop species beforehand; (2) the improvement is superior when applying multiple linear regression using three explanatory SI's approach. In addition to linear investigations, we applied the non-linear CART (Classification and Regression Trees) technique, which finally did not show the potential for any improvement in the retrieval process

Incorporating Multiresolution Analysis With Multiclassifiers And Decision Fusion For Hyperspectral Remote Sensing

The ongoing development and increased affordability of hyperspectral sensors are increasing their utilization in a variety of applications, such as agricultural monitoring and decision making. Hyperspectral Automated Target Recognition (ATR) systems typically rely heavily on dimensionality reduction methods, and particularly intelligent reduction methods referred to as feature extraction techniques. This dissertation reports on the development, implementation, and testing of new hyperspectral analysis techniques for ATR systems, including their use in agricultural applications where ground truthed observations available for training the ATR system are typically very limited. This dissertation reports the design of effective methods for grouping and down-selecting Discrete Wavelet Transform (DWT) coefficients and the design of automated Wavelet Packet Decomposition (WPD) filter tree pruning methods for use within the framework of a Multiclassifiers and Decision Fusion (MCDF) ATR system. The efficacy of the DWT MCDF and WPD MCDF systems are compared to existing ATR methods commonly used in hyperspectral remote sensing applications. The newly developed methods’ sensitivity to operating conditions, such as mother wavelet selection, decomposition level, and quantity and quality of available training data are also investigated. The newly developed ATR systems are applied to the problem of hyperspectral remote sensing of agricultural food crop contaminations either by airborne chemical application, specifically Glufosinate herbicide at varying concentrations applied to corn crops, or by biological infestation, specifically soybean rust disease in soybean crops. The DWT MCDF and WPD MCDF methods significantly outperform conventional hyperspectral ATR methods. For example, when detecting and classifying varying levels of soybean rust infestation, stepwise linear discriminant analysis, results in accuracies of approximately 30%-40%, but WPD MCDF methods result in accuracies of approximately 70%-80%

Incorporating Multiresolution Analysis With Multiclassifiers And Decision Fusion For Hyperspectral Remote Sensing

The ongoing development and increased affordability of hyperspectral sensors are increasing their utilization in a variety of applications, such as agricultural monitoring and decision making. Hyperspectral Automated Target Recognition (ATR) systems typically rely heavily on dimensionality reduction methods, and particularly intelligent reduction methods referred to as feature extraction techniques. This dissertation reports on the development, implementation, and testing of new hyperspectral analysis techniques for ATR systems, including their use in agricultural applications where ground truthed observations available for training the ATR system are typically very limited. This dissertation reports the design of effective methods for grouping and down-selecting Discrete Wavelet Transform (DWT) coefficients and the design of automated Wavelet Packet Decomposition (WPD) filter tree pruning methods for use within the framework of a Multiclassifiers and Decision Fusion (MCDF) ATR system. The efficacy of the DWT MCDF and WPD MCDF systems are compared to existing ATR methods commonly used in hyperspectral remote sensing applications. The newly developed methods’ sensitivity to operating conditions, such as mother wavelet selection, decomposition level, and quantity and quality of available training data are also investigated. The newly developed ATR systems are applied to the problem of hyperspectral remote sensing of agricultural food crop contaminations either by airborne chemical application, specifically Glufosinate herbicide at varying concentrations applied to corn crops, or by biological infestation, specifically soybean rust disease in soybean crops. The DWT MCDF and WPD MCDF methods significantly outperform conventional hyperspectral ATR methods. For example, when detecting and classifying varying levels of soybean rust infestation, stepwise linear discriminant analysis, results in accuracies of approximately 30%-40%, but WPD MCDF methods result in accuracies of approximately 70%-80%

Selection of the key earth observation sensors and platforms focusing on applications for Polar Regions in the scope of Copernicus system 2020-2030

An optimal payload selection conducted in the frame of the H2020 ONION project (id 687490) is presented based on the ability to cover the observation needs of the Copernicus system in the time period 2020–2030. Payload selection is constrained by the variables that can be measured, the power consumption, and weight of the instrument, and the required accuracy and spatial resolution (horizontal or vertical). It involved 20 measurements with observation gaps according to the user requirements that were detected in the top 10 use cases in the scope of Copernicus space infrastructure, 9 potential applied technologies, and 39 available commercial platforms. Additional Earth Observation (EO) infrastructures are proposed to reduce measurements gaps, based on a weighting system that assigned high relevance for measurements associated to Marine for Weather Forecast over Polar Regions. This study concludes with a rank and mapping of the potential technologies and the suitable commercial platforms to cover most of the requirements of the top ten use cases, analyzing the Marine for Weather Forecast, Sea Ice Monitoring, Fishing Pressure, and Agriculture and Forestry: Hydric stress as the priority use cases.Peer ReviewedPostprint (published version

Detection of leek rust disease under field conditions using hyperspectral proximal sensing and machine learning

Rust disease is an important problem for leek cultivation worldwide. It reduces market value and in extreme cases destroys the entire harvest. Farmers have to resort to periodical full-field fungicide applications to prevent the spread of disease, once every 1 to 5 weeks, depending on the cultivar and weather conditions. This implies an economic cost for the farmer and an environmental cost for society. Hyperspectral sensors have been extensively used to address this issue in research, but their application in the field has been limited to a relatively low number of crops, excluding leek, due to the high investment costs and complex data gathering and analysis associated with these sensors. To fill this gap, a methodology was developed for detecting leek rust disease using hyperspectral proximal sensing data combined with supervised machine learning. First, a hyperspectral library was constructed containing 43,416 spectra with a waveband range of 400-1000 nm, measured under field conditions. Then, an extensive evaluation of 11 common classifiers was performed using the scikit-learn machine learning library in Python, combined with a variety of wavelength selection techniques and preprocessing strategies. The best performing model was a (linear) logistic regression model that was able to correctly classify rust disease with an accuracy of 98.14%, using reflectance values at 556 and 661 nm, combined with the value of the first derivative at 511 nm. This model was used to classify unlabelled hyperspectral images, confirming that the model was able to accurately classify leek rust disease symptoms. It can be concluded that the results in this work are an important step towards the mapping of leek rust disease, and that future research is needed to overcome certain challenges before variable rate fungicide applications can be adopted against leek rust disease